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View Structure Prediction Details

Protein: PAP2
Organism: Saccharomyces cerevisiae
Length: 584 amino acids
Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076



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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for PAP2.

Description E-value Query
Range
Subject
Range
PAP2 - Non-canonical poly(A) polymerase, involved in nuclear RNA degradation as a component of the TRAMP co...
PAP2_YEAST - Poly(A) RNA polymerase protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PAP2 PE...
0.0 [1..584] [1..584]
TRF5_ASHGO - Poly(A) RNA polymerase protein 1 OS=Ashbya gossypii GN=TRF5 PE=3 SV=1
TRF5_ASHGO - Poly(A) RNA polymerase protein 1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NR...
0.0 [4..549] [24..558]
gi|7507776 - gi|7507776|pir||T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans
3.0E-99 [20..490] [674..1125]
ENSPTRT00000012343 - null
PAPOLA - poly(A) polymerase alpha
4.0E-95 [144..537] [2..433]
gi|447739 - gi|447739|prf||1915304A nylB upstream ORF
1.0E-94 [144..537] [2..433]
gi|120538567, gi... - gi|9910588|ref|NP_064327.1| poly(A) polymerase beta (testis specific) [Mus musculus], gi|5701744|dbj...
1.0E-94 [144..537] [3..434]

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Predicted Domain #1
Region A:
Residues: [1-116]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGAKSVTASS SKKIKNRHNG KVKKSKKIKK VRKPQKSISL NDENEVEILP SRNEQETNKL  60
   61 PKDHVTADGI LVLEHKSDDD EGFDVYDGHF DNPTDIPSTT EESKTPSLAV HGDEKD

[Run NCBI BLAST on this sequence.]

Detection Method: deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2
Region A:
Residues: [117-192]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LANNDDFISL SASSEDEQAE QEEEREKQEL EIKKEKQKEI LNTDYPWILN HDHSKQKEIS  60
   61 DWLTFEIKDF VAYISP

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [304-584]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AAKLIREWLD DTPGLRELVL IVKQFLHARR LNNVHTGGLG GFSIICLVFS FLHMHPRIIT  60
   61 NEIDPKDNLG VLLIEFFELY GKNFGYDDVA LGSSDGYPVY FPKSTWSAIQ PIKNPFSLAI 120
  121 QDPGDESNNI SRGSFNIRDI KKAFAGAFDL LTNRCFELHS ATFKDRLGKS ILGNVIKYRG 180
  181 KARDFKDERG LVLNKAIIEN ENYHKKRSRI IHDEDFAEDT VTSTATATTT DDDYEITNPP 240
  241 AKKAKIEEKP ESEPAKRNSG ETYITVSSED DDEDGYNPYT L

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 91.0
Match: 1f5aA_
Description: Poly(A) polymerase, middle domain; Poly(A) polymerase N-terminal, catalytic domain; Poly(A) polymerase, C-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
nucleic acid binding 2.13067754075302 bayes_pls_golite062009
nucleotidyltransferase activity 2.12021443504286 bayes_pls_golite062009
binding 2.05218701326405 bayes_pls_golite062009
RNA binding 1.77578561123536 bayes_pls_golite062009
polynucleotide adenylyltransferase activity 1.54779952898232 bayes_pls_golite062009
DNA binding 1.5286843489086 bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups 1.08480919674453 bayes_pls_golite062009
DNA-directed DNA polymerase activity 0.773960702302769 bayes_pls_golite062009
catalytic activity 0.75232920999699 bayes_pls_golite062009
DNA polymerase activity 0.739770356253601 bayes_pls_golite062009
transferase activity 0.432029324907561 bayes_pls_golite062009
transcription factor binding 0.227209369499116 bayes_pls_golite062009
protein binding 0.0181192131028179 bayes_pls_golite062009

Predicted Domain #3
Region A:
Residues: [193-303]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SREEIEIRNQ TISTIREAVK QLWPDADLHV FGSYSTDLYL PGSDIDCVVT SELGGKESRN  60
   61 NLYSLASHLK KKNLATEVEV VAKARVPIIK FVEPHSGIHI DVSFERTNGI E

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 91.0
Match: 1f5aA_
Description: Poly(A) polymerase, middle domain; Poly(A) polymerase N-terminal, catalytic domain; Poly(A) polymerase, C-terminal domain
Matching Structure (courtesy of the PDB):

YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle